Wakefield wrote A Reply to Some Parts of the Bishop Llandaff's Address to the People of Great Britain, a Unitarian work attacking the privileged position of the wealthy. This was in response to An Address to the People of Great Britain (1798), by Richard Watson, Bishop of Llandaff, which argues that national taxes should be raised to pay for the war against France and to reduce the national debt. Johnson and others were put on trial for sedition for selling Wakefield's Reply. Johnson was fined £50 and sentenced to six months imprisonment at King's Bench Prison in February 1799, after which he published very few political works and no controversial ones.

Towards the end of 1791 appeared Wakefield's Translation of the New Testament, with Notes, in three volumes octavos. In his memoirs Wakefield records that the work was laborious particularly in the comparison of the Oriental versions with the received text, but was well received and "much more profitable to me than all my other publications put together".[3] A revised edition followed in 1795.

Wakefield also published editions of various classical writers, and among his theological writings are Early Christian Writers on the Person of Christ (1784), Silva Critica (1789–95), illustrations of the Scriptures, and An Examination of Paine's Age of Reason in (1794).